• Virtual EchinoClub

    Hope you can join us!

    When you register we will have your email to send the link the day before the meeting.

    If you have registered for a previous meeting you do not need to register again.

    New registrations please email to Echinobase@andrew.cmu.edu to be added to the list.

    Read More...

  • 2024 Echinobase Citation

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  • FAQs - Gene Names and IDs

    Discovery of new genes, or analysis of current genes sometimes leads to gene nomenclature questions.

    Genome-wide studies involving transcripts and proteins require related IDs.

    Here we have listed a few of the more common questions.

    Read More...

  • FAQs - General

    Trying to find information?

    Check the FAQs!

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  • Alignment is the Ground Truth

    BLAST your sequences for primers, probes and morpholinos to check where they align.

    Keep your data updated!!

     

    Read More...

  • Echinobase Identifiers

     

    Echinobase identifiers have been updated.

    Suggestions for finding your gene of interest and using the new identifiers are available in this

    video tutorial.

     

     

    Read More...

  • The Echinoderm Anatomical Ontology (ECAO)

     

    An ontology has been developed for echinoderms using standardized terms to describe anatomical cell types and structures and developmental stages.

     

    These spatiotemporal terms will be used by curators to link to gene expression data.

     

     

    Read More...

  • Echinoderms are Deuterostomes

     

    The superphylum

    Deuterostomia includes

    Chordata, 

    Echinodermata and

    Hemichordata phyla.

    Echinodermata includes

    marine only species,

    7,000 extant and

    13,000 extinct. 

    . 

    Read More...

  • Virtual EchinoClub

    Hope you can join us!

    When you register we will have your email to send the link the day before the meeting.

    If you have registered for a previous meeting you do not need to register again.

    New registrations please email to Echinobase@andrew.cmu.edu to be added to the list.

    Read More...
Latest Echinobase Content
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Genes & Expression
Genome Browsers

Browse genomes and community contributed datasets. If you find a dataset missing or have a new dataset to contribute for a supported genome please contact us!

[+]S. purpuratus (Purple sea urchin) v.5.0

  S. purpuratus v.4.2

  S. purpuratus v.3.1

L. variegatus (Green sea urchin) v.3.0

P. miniata (Bat star) v.3.0

A. planci (Crown-of-thorns) v.1.0

L. pictus (Painted urchin) v.2.1

A. rubens (Sugar star) v.1.3

A. japonica (Feather star) v.1.0

EchinoBLAST

BLAST Echinoderm nucleotide and protein databases.

S. purpuratus (Purple sea urchin):
   Genome, RNA, Proteins, CDS

L. variegatus (Green sea urchin):
   Genome RNA, Proteins, CDS

P. miniata (Bat star):
   Genome , RNA, Proteins, CDS

A. planci (Crown-of-thorns):
   Genome, RNA, Proteins, CDS

L. pictus (Painted urchin):
   Genome

A. rubens (Sugar star):
   Genome

A. japonica (Feather star):
   Genome
Deuterostomia (superphylum) includes Chordata, Echinodermata and Hemichordata phylum, Echinodermata emerged in the Lower Cambrian (> 540 million years ago, MYA) and split from Chordata 400-500 MYA, Echinodermata includes 7,000 extant and 13,000 extinct, marine only species. Echinodermata has 5 Classes: the basal branching Crinoidea (crinoids), and the 4 motile Eleutherozoa Classes including Asterozoa, the Ophiuroidea (brittle stars) and Asteroidea (starfish) and the Echinozoa, the Echinoidea (sea urchins and sand dollars) and Holotheroidea (sea cucumber).

Echinoderms are model organisms for studying embryo development and regeneration due to many unique features including:
  • the ability to synchronize fertilization of millions of eggs
  • transparent embryos and larvae
  • varied development within and between a genus
Echinobase supports the international research community by providing a centralized, integrated and easy to use web based resource to access the diverse and rich, functional genomics data of echinoderm species.

Echinobase is organized around the GENEPAGE which displays information about genes, orthology, and links to research papers. The gene models of echinoderm species are associated with the genome sequence using the genome browser, JBrowse. Temporal developmental gene expression data will be displayed when available, and spatial cell type information will be associated using the Echinoderm Anatomical Ontology (ECAO).

Echinobase provides a critical data sharing infrastructure for other NIH-funded projects. In addition to our primary goal of supporting echinoderm researchers, Echinobase enhances the availability and visibility of echinoderm data to the broader biomedical research community.

Species in Echinobase are divided into two categories:
fully supported species found on gene pages and partially supported species that only have support through the genome browser and BLAST processes. We are an expanding resource and both species sets will grow in upcoming months and years.

More About Echinobase
S. purpuratus
Strongylocentrotus purpuratus (the purple sea urchin)
The purple sea urchin, Strongylocentrotus purpuratus, lives in lower intertidal and nearshore subtidal communities along the eastern edge of the Pacific Ocean extending from Ensenada, Mexico to British Columbia, Canada. Morphological development of S. purpuratus from embryo to adult has been studied for over 100 years and recent decades have added genetic and genomic data to our knowledge of this model organism.

The substantially improved current release of the purple sea urchin genome assembly (Spur5.0) is sixth in the series.

Learn more about the genomics of the purple sea urchin.

L. pictus
Image credit: Katherine Nesbit, UC San Diego https://pubmed.ncbi.nlm.nih.gov/32644271/
Lytechinus pictus (painted urchin)
Lytechinus pictus, the painted urchin, lives in the shallow reefs off the Pacific coasts of California and Mexico. This sea urchin is small, only 40 mm (1.6 in) in diameter. The general color is white or pale straw brown, sometimes pinkish. L. pictus is being developed as a genetically-enabled sea urchin model. Genetic lines of L. pictus have been generated with stable modifications that are useful for cell and developmental studies as well as physiological studies and drug screens.

A. japonica
Anneissia japonica (feather star)
​The crinoids are sessile and include feather stars, which do not have a stalk, and sea lilies which are attached to the sea floor by a stalk. Feather stars are most abundant in shallow, rocky waters of the Indian and western Pacific oceans. As plankton flows by the feather-like arms it sticks to a mucus secreted by the tube feet and these particles are moved towards the mouth. Species of crinoids are used as an outgroup for phylogenetic studies within the Echinodermata.

A. rubens
Asterias rubens (sugar star or the common sea star)
​The sugar star is the most familiar and common sea star in the northern Atlantic coastal waters, living on rocky and gravelly surfaces. The five arms are orange or brownish in color and span 10-30 cm. Sugar stars feed on molluscs, polychaete worms and barnacles and can be preyed upon by the common sunstar.

P. miniata
Patiria miniata (the bat star)
The bat star, Patiria miniata, (formerly called Asterina miniata) is a common sea star found along the Pacific coastline of North America from southern Alaska to the Gulf of California, Mexico, in intertidal and subtidal locations to depths of 300 m. Bat stars typically have 5 arms but range from 3 to 8 and can be red, orange, brown, yellow, blue, pink, green, and intermediate color and adults are about 8 inches across. P. miniata reproduce by broadcast spawning and embryos hatch into planktonic larvae and later metamorphose into pentaradial juveniles which develop into young sea stars with stubby arms.

The current version, v3.0, of the assembly is fully supported at Echinobase.

Learn more about the genomics of the bat star.

L. variegatus
Lytechinus variegatus (the green sea urchin)
Lytechinus variegatus (Lamarck, 1816) is known as the green sea urchin or variegated sea urchin. It has many color morphs including white, green, purple, red, or pink or a combination of those colors. Multiple subspecies inhabit distinct geographical territories of the western Atlantic tropics ranging from North Carolina south to the Carribean, Gulf of Mexico and northern Brazil. The planktonic larvae are known as pluteus larvae that metamorphose to juvenile urchins.

The L. variegatus v3.0 genome is the first echinoderm assembly with chromosomal resolution.

Learn more about the genomics of the green sea urchin.

A. planci
Acanthaster planci (the crown-of-thorns seastar)
The crown-of-thorns seastar (COTS), Acanthaster planci, is is named for the spines that cover the top of its large body and multiple arms. A. planci lives in Indo-Pacific waters and preys upon corals. Outbreaks where large numbers of COTS aggregate can decimate coral reefs. Due to their destructive nature the genome was sequenced in the search for biocontrol strategies. The current version of the A. planci genome, v1.0, is available on Echinobase.

Learn more about the genomics of the crown-of-thorns seastar.

Echinoderms are marine organisms that when harvested from the wild, can live in aquariums and embryo and larval development has been studied for over 100 years. Echinoderm eggs are fertilized externally and embryos and larvae are transparent, enabling detailed descriptions of the structure and timing of development.

The variation and comparison of developmental patterns of related species is used to improve understanding of these vital processes and their evolution in echinoderms and deuterostomes. Echinoderms are models for studies of skeletogenesis and regeneration.

The Echinoderm Anatomical Ontology (ECAO) provides standardized terms for developmental stages for S. purpuratus, and is being expanded to include additional echinoderm species.

For studies of regulatory sequences BAC Libraries are available. Refer to the BAC Table for those that can been identified using BAC-ENDs and the genome browser or screen the BAC library for your gene of interest. An in-frame fusion of a reporter gene can be engineered into the locus of interest by recombineering to assess gene expression and putative regulatory sequences.

Echinobase automatically searches the scientific literature and collects articles related to echinoderms. Users can come to the site to access currently available published research in one centralized location. Papers are manually curated to link genomic information to protocols and reagents for future studies.

Echinobase has collected contact information for members of the community and is working to maintain a current, updated web interface, for accessing and querying genomes, transcriptomes, chromatin structure, regulation and expression of genes during development with documentation, and supporting information, an image database, and robust ontologies.

Community members are welcomed to contribute to EchinoWiki with protocols, reagents and data, and to submit new genomes for partial or full support.

Genomes are eligible for partial support when assembly and annotation are publicly available through Genbank. The assemblies, annotations, and functional data tracks (GFF files) will be available on the JBrowse genome browser and can be searched via BLAST.

The Echinobase PIs and SAB members will decide the new species for full support and integration into the database as gene pages with complete functionality, including gene names and symbols, synonyms, literature, orthology, and developmental gene expression display. This process will only be possible when the genome has been fully processed by the NCBI annotation pipeline. Suggestions for priority species are always welcome.